If that solution applies to the original model you used (and not to re-solving the structure with the molecular replacement solution before or after refinement), then your tetramer model is just being rotated by 90 degrees around the 4-fold and placed on a different origin, i.e. the solution is equivalent to the starting model, except for applying symmetry and a change of origin.
If that's true, then it implies that this is an isomorphous crystal to the one giving the model you're using for molecular replacement. Is that crystal in P41 with similar cell dimensions? Rigid-body refinement would be a sensible option in such a case, with the advantage that your new model is guaranteed to be on the same origin and thus easier to compare with the old model. Getting to the main question, you really have to look at the result of twinning tests. If they suggest that your crystal is twinned, then it's probably P41 with the twinning increasing the apparent symmetry of the data. But it's important to look at all the evidence, not just the Rfree after refinement, especially as the application of a twin target always lowers Rfree. Best wishes, Randy Read ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 Wellcome Trust/MRC Building Fax: +44 1223 336827 Hills Road E-mail: [email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk On 1 Dec 2012, at 00:59, ruisher hu wrote: > Hi, Dear CCP4 group, > > I recently collect one dataset and indexed as P4 space group. When I try to > do MR with a tetramer as input, I found the solution file suggested P41. > > SOLU SET RFZ=5.2 TFZ=10.3 PAK=0 LLG=239 LLG=366 TFZ==20.9 > SOLU SPAC P 41 > SOLU 6DIM ENSE ensemble1 EULER 50.265 0.217 219.800 FRAC 0.50029 0.49916 > -0.00408 BFAC -0.04000 > SOLU ENSE ensemble1 VRMS 0.639 > SOLU SET RFZ=5.2 TFZ=10.0 PAK=0 LLG=239 TFZ==11.2 LLG=365 > SOLU SPAC P 41 > SOLU 6DIM ENSE ensemble1 EULER 128.607 179.813 38.677 FRAC 0.49991 0.49905 > -0.00208 BFAC -0.06264 > SOLU ENSE ensemble1 VRMS 0.642 > > However when I did refinement in phenix, I have some trouble getting the > R/Rfree down. It complains about some twinning or maybe higher symmetry like > P422. When I apply twin law, h,-k,-l, I'm able to refine to 0.34/0.37 but > still, hard to continue the refinement. The strategy I used for refinement is > xyz coordinates, real-space, individual B-factors, occupancies, with NCS > restraints and twin law. > > So I tried to rescaled into P41212 space group, and run MR again, with two > chains as an input and found one solution > SOLU SET RFZ=4.5 TFZ=9.5 PAK=0 LLG=115 TFZ==10.0 LLG=118 TFZ==10.4 > SOLU SPAC P 41 21 2 > SOLU 6DIM ENSE ET EULER 234.6 0.7 305.0 FRAC 1.00 0.49 -0.17 BFAC -0.14 > Ensemble ET RMS variance(s): 0.96 > > However, when i tried to refine, the Rfree is high as 0.51 at the first > round. Does this mean this is not the right solution or maybe some problems > with the space group?Any suggestions for next step? Thanks very much. > >
